E-infrastructure

The platform ABiMS aims to develop and provide infrastructures for analysis purposes. Those e-Infrastructures are composed of different types of components:

The Hardware is mainly composed around a High Performance Computer constituted of 1600 CPU. Jobs are submitted through a scheduler (SGE). Other layers can be added like virtualization servers to host applications on dedicated and isolated virtual machine (VM).

Some public Databanks like genomics resources (GenBank, Uniprot, …) are provided (/db/) to different applications (CLI software, Galaxy workflows) in several indexing formats (Blast, Bowtie, BWA, …). Most of them are automatically downloaded and formatted using BioMAJ.

The platform, since 2012, is strongly involved in the Virtual Research Environment (VRE) Galaxy. ABiMS takes part in different national initiatives (with the working group IFB-Galaxy) and international initiatives (with the Elixir Galaxy Group). The platform takes part also in the organisation of workshops and conferences (GCC2017) and in the Galaxy developments with the project Workflow4Metabolomics, the Galaxy Training Materials, with some hacks in IUC Tools, and some minor commits in Planemo and Galaxy itself.

Furthermore, we maintain several open access Galaxy instances (see: Resources / Galaxy)

We also propose, through collaborations, some genome browsers (JBrowse) and collaborative genomic annotation editors (Apollo) from the GMOD project.